Well, I dunno if this counts, but I'm currently beta-reading a fic that started out with some very Sue-y characters, but they've since become more logical and well-written, I think.

Her name was Jacqueline Lantern and she was a Rise of the Guardians Sue. She was Spirit of Halloween. She was an angsty!Sue until I looked back and realized how much fun writing psychopaths is.

I was working on a story like that. It's not for my Agents, which I will eventually submit...
It's about a Sue who gains self-awareness about what she is doing and the whole hierarchy of Suvians...

I could really use a beta, is anyone willing to help me out?

Of course, the things that were wrong with my Mary Sue were all the added things (like cool stuff TM) that were taking away from having an actual plot and characterization, so once I dumped the merchandise and worked with her a few more years, I got a character who turned up under different names in five different unfinished stories. She's the mother of one of my main characters in this year's mystery novel, actually. (And although he's nearly unrecognizable now compared to when I was twelve, her elf prince boyfriend stuck with her all this time and is her husband & the MC's father.)

I've had those two since I was twelve or so, and I'm turning twenty two on the seventeenth, so it's safe to say that they've changed a lot. I also learned quite a bit in the intervening years.

(For bonus points, Sierra started as an Abhorsen-but-not because I didn't know fan-fiction existed at the time. At some point she returned to her origins and became a benevolent necromanceress who gives lost souls a voice so they can pass on. She also did some time as Gandalf the Grey's apprentice, under the name Yara Greencloak, and has been transplanted to at least three original worlds. :D)

A few years ago, when I was just starting out with writing, I made a horrid little God-Modder Stu. After a while, I forgot about him. A while after that, I realized exactly what I'd been writing, and in horror, annihilated the story from every database I could find it on.

Then, after I discovered the PPC, the idea of that Stu resurfaced, and I was tempted to bring him back just to kill him. But instead I decided to give his character a complete overhaul, and turned him into Agent Legacy, who has permission, but hasn't been written yet.

So. Er… Yeah, I suppose that counts. :)

Because most Sues tend to be surprisingly powerless. Unless it helps them get their "hott man".

Or, you know, maybe it's because I work in the BBC Sherlock verse pretty often. Sues there have a very common 'power' termed superdeduction, which, as we all know, is honed through observation and is most definitely not genetic.

Anyway. Most of my Agents are reformed Sues in a meta sense. Lori Starrett even had her own fic that almost got published disguised as a goodfic that was getting debunked by more blatant Sues, but only Trojie and Pads were aware of it since they looked it over and caught me before I published. And then from there it's a simple matter of just completely rewriting her backstory so that she doesn't originate from Middle-earth like previously, but from Earth with a keen interest in Tolkien, etc.

And Agent Eledhwen used to be way more Suvian as well. She was more or less a one-sided drama queen (or as I termed it, 'emo') and a cardboard foil to an Agent Lily who was, putting it nicely, hyperactive. A bit of that remains to this day in the form of Eledhwen's clone Lilith from the Mary Sue Factories, who got killed in IAHF1.

He was a Gary Stu. Now his reaction to one is "kill him".